Preheat oven to 350°F.
Make flax egg by mixing together flaxseed and water and set aside.
In a big bowl, mash the bananas with a fork. Set aside.
Cream together the peanut butter and sugar.
Mix together the remaining dry ingredients.
Add the flax egg, vanilla, vinegar, and milk to the peanut butter/sugar mixture. Mix well, then add this to the bananas and combine.
Add half the dry ingredients into wet and stir till almost combined. Add the remaining dry ingredients and stir till just combined. Add the chocolate chips and mix lightly, just until chocolate chips are evenly distributed.
Bake for 18 minutes, or until a toothpick inserted into the center of a muffin comes out clean. Let cool at least 20 minutes.